ExomeHMM: A Hidden Markov Model for Detecting Copy Number Variation Using Whole-Exome Sequencing Data

Abstract

Background: Copy number variations (CNVs), including amplification and deletion, are alterations of DNA copy number compared to a reference genome. CNVs play a crucial role in tumourigenesis and progression, including amplification of oncogenes and deletion of tumor suppressor genes that may significantly increase the risk of cancer. CNVs are also reported to be closely related with non-cancer diseases, such as Down syndrome, Parkinson disease, and Alzheimer disease. Keywords: Copy number variation, expectation–maximization algorithm, hidden Markov model, next generation sequencing, viterbi algorithm, whole-exome sequencing.